run_pfam_scan.sh uses obsolete -pfamB option

[peterjc]

According to discussion in #6 these scripts should work with recent Pfam releases using HMMER3 and a recent pfam_scan.pl.

However, the current version of bash_scripts/run_pfam_scan.sh when calling pfam_scan.pl v1.6 fails, it aborts with the message:

FATAL: As of release 28.0, Pfam no longer produces Pfam-B. The -pfamB and -only_pfamB options are now obsolete.

It is trivial to remove -pfamB from bash_scripts/run_pfam_scan.sh but does this break any downstream assumptions in the pipeline?

[krasileva]

Hi Peter,

You can safely remove it. We did not use PfamB in downstream analyses, so it is a leftover from testing it during pfamscan step. The downstream scripts have ‘skip PfamB’ in them, which would become unnecessary but would not break anything.

Best wishes,

Ksenia

---

Ksenia Krasileva Group Leader

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Norwich Research Park Norwich Norfolk NR4 7UZ +44 (0) 1603 450 2946 Ksenia.Krasileva@earlham.ac.ukmailto:Ksenia.Krasileva@earlham.ac.uk

www.earlham.ac.uk/krasileva-grouphttp://www.earlham.ac.uk/krasileva-group www.tsl.ac.uk/groups/krasileva-grouphttp://www.tsl.ac.uk/groups/krasileva-group @kseniakrasileva

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From: Peter Cock notifications@github.com Reply-To: krasileva-group/plant_rgenes reply@reply.github.com Date: Monday, 20 November 2017 at 11:59 To: krasileva-group/plant_rgenes plant_rgenes@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [krasileva-group/plant_rgenes] run_pfam_scan.sh uses obsolete -pfamB option (#8)

According to discussion in #6https://github.com/krasileva-group/plant_rgenes/issues/6 these scripts should work with recent Pfam releases using HMMER3 and a recent pfam_scan.pl.

However, the current version of bash_scripts/run_pfam_scan.sh when calling pfam_scan.pl v1.6 fails, it that aborts with the message:

FATAL: As of release 28.0, Pfam no longer produces Pfam-B. The -pfamB and -only_pfamB options are now obsolete.

It is trivial to remove -pfamB from bash_scripts/run_pfam_scan.sh but does this break any downstream assumptions in the pipeline?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/krasileva-group/plant_rgenes/issues/8, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AB2D2F0-2wRWVBCtUqg_ZTEIDjzl8VWYks5s4Wm4gaJpZM4QkJ29.

[peterjc]

Thanks - that's good news.

Are you able to update this repository yourself and/or merge pull requests?

[krasileva]

Hi Peter,

Technically, yes, but I find myself without a minute to do this at the moment because I am at home with sick kids. Would you like to join as collaborator? you have so many useful suggestions so I think the project will benefit from your formal input.

Best wishes,

Ksenia

---

Ksenia Krasileva Group Leader

[cid:image001.png@01D361FD.28901DF0]

Norwich Research Park Norwich Norfolk NR4 7UZ +44 (0) 1603 450 2946 Ksenia.Krasileva@earlham.ac.ukmailto:Ksenia.Krasileva@earlham.ac.uk

www.earlham.ac.uk/krasileva-grouphttp://www.earlham.ac.uk/krasileva-group www.tsl.ac.uk/groups/krasileva-grouphttp://www.tsl.ac.uk/groups/krasileva-group @kseniakrasileva

www.earlham.ac.ukhttp://www.earlham.ac.uk/ www.tsl.ac.ukhttp://www.tsl.ac.uk/

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From: Peter Cock notifications@github.com Reply-To: krasileva-group/plant_rgenes reply@reply.github.com Date: Monday, 20 November 2017 at 12:10 To: krasileva-group/plant_rgenes plant_rgenes@noreply.github.com Cc: "Ksenia Krasileva (EI)" Ksenia.Krasileva@earlham.ac.uk, Comment comment@noreply.github.com Subject: Re: [krasileva-group/plant_rgenes] run_pfam_scan.sh uses obsolete -pfamB option (#8)

Thanks - that's good news.

Are you able to update this repository yourself and/or merge pull requests?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/krasileva-group/plant_rgenes/issues/8#issuecomment-345677963, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AB2D2Dw1uzc6bFEfYH1NUIO9x71-dsV8ks5s4WwxgaJpZM4QkJ29.

[peterjc]

I'll decline the kind GitHub collaborator status offer (for now at least), but will submit a few pull requests for you to look at later when you have time back in the office - no rush.

[krasileva]

Hi Peter,

Ok. I appreciate all of your comments!

Best wishes,

Ksenia

---

Ksenia Krasileva Group Leader

[cid:image001.png@01D36204.161BFAC0]

Norwich Research Park Norwich Norfolk NR4 7UZ +44 (0) 1603 450 2946 Ksenia.Krasileva@earlham.ac.ukmailto:Ksenia.Krasileva@earlham.ac.uk

www.earlham.ac.uk/krasileva-grouphttp://www.earlham.ac.uk/krasileva-group www.tsl.ac.uk/groups/krasileva-grouphttp://www.tsl.ac.uk/groups/krasileva-group @kseniakrasileva

www.earlham.ac.ukhttp://www.earlham.ac.uk/ www.tsl.ac.ukhttp://www.tsl.ac.uk/

[cid:image002.png@01D36204.161BFAC0]https://twitter.com/EarlhamInst[cid:image003.png@01D36204.161BFAC0]https://www.facebook.com/EarlhamInst/

From: Peter Cock notifications@github.com Reply-To: krasileva-group/plant_rgenes reply@reply.github.com Date: Monday, 20 November 2017 at 13:31 To: krasileva-group/plant_rgenes plant_rgenes@noreply.github.com Cc: "Ksenia Krasileva (EI)" Ksenia.Krasileva@earlham.ac.uk, Comment comment@noreply.github.com Subject: Re: [krasileva-group/plant_rgenes] run_pfam_scan.sh uses obsolete -pfamB option (#8)

I'll decline the kind GitHub collaborator status offer (for now at least), but will submit a few pull requests for you to look at later when you have time back in the office - no rush.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/krasileva-group/plant_rgenes/issues/8#issuecomment-345695929, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AB2D2I5Mcc3Xf2DSoTEJ_PZB-iXZJ_Hjks5s4X8xgaJpZM4QkJ29.

[peterjc]

Fixed via #9